Hi all - It looks like bowtie's wrapper is working incorrectly for a list
of dataset pairs.  Its expecting all the forward reads in one dataset list
and the reverse reads in a separate dataset list.

Instead, I have a list of dataset pairs (for paired-end data).  This cannot
be provided to bowtie as input.  If I correct this, should I create a pull
request for it?  Alternatively, does someone already have a corrected
version of this?
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